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- PDB-6y4r: Cytoplasmic domain of TssL from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 6y4r
TitleCytoplasmic domain of TssL from Acinetobacter baumannii
ComponentsDotU family type IV/VI secretion system protein
KeywordsUNKNOWN FUNCTION / Component of the T6SS
Function / homologyType IV / VI secretion system, DotU / Type IV / VI secretion system, DotU superfamily / Type VI secretion system protein DotU / DotU family type IV/VI secretion system protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.594 Å
AuthorsRuiz, F.M. / Romero, A.
CitationJournal: J.Bacteriol. / Year: 2020
Title: Structural Characterization of TssL from Acinetobacter baumannii: a Key Component of the Type VI Secretion System.
Authors: Ruiz, F.M. / Lopez, J. / Ferrara, C.G. / Santillana, E. / Espinosa, Y.R. / Feldman, M.F. / Romero, A.
History
DepositionFeb 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DotU family type IV/VI secretion system protein
B: DotU family type IV/VI secretion system protein
C: DotU family type IV/VI secretion system protein
D: DotU family type IV/VI secretion system protein
E: DotU family type IV/VI secretion system protein
F: DotU family type IV/VI secretion system protein


Theoretical massNumber of molelcules
Total (without water)112,6956
Polymers112,6956
Non-polymers00
Water4,468248
1
A: DotU family type IV/VI secretion system protein


Theoretical massNumber of molelcules
Total (without water)18,7821
Polymers18,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DotU family type IV/VI secretion system protein


Theoretical massNumber of molelcules
Total (without water)18,7821
Polymers18,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DotU family type IV/VI secretion system protein


Theoretical massNumber of molelcules
Total (without water)18,7821
Polymers18,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DotU family type IV/VI secretion system protein


Theoretical massNumber of molelcules
Total (without water)18,7821
Polymers18,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: DotU family type IV/VI secretion system protein


Theoretical massNumber of molelcules
Total (without water)18,7821
Polymers18,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: DotU family type IV/VI secretion system protein


Theoretical massNumber of molelcules
Total (without water)18,7821
Polymers18,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.845, 78.835, 96.968
Angle α, β, γ (deg.)90.000, 119.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 3:31 or resseq 33:39 or resseq...
21(chain B and (resseq 3:31 or resseq 33:39 or resseq...
31(chain C and (resseq 3:31 or resseq 33:39 or resseq...
41(chain D and (resseq 3:31 or resseq 33:39 or resseq...
51(chain E and (resseq 3:31 or resseq 33:39 or resseq...
61(chain F and (resseq 3:31 or resseq 33:39 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 3:31 or resseq 33:39 or resseq...A3 - 31
121(chain A and (resseq 3:31 or resseq 33:39 or resseq...A33 - 39
131(chain A and (resseq 3:31 or resseq 33:39 or resseq...A41 - 42
141(chain A and (resseq 3:31 or resseq 33:39 or resseq...A44 - 78
151(chain A and (resseq 3:31 or resseq 33:39 or resseq...A1 - 160
161(chain A and (resseq 3:31 or resseq 33:39 or resseq...A111 - 115
171(chain A and (resseq 3:31 or resseq 33:39 or resseq...A1 - 160
181(chain A and (resseq 3:31 or resseq 33:39 or resseq...A139
191(chain A and (resseq 3:31 or resseq 33:39 or resseq...A1 - 160
1101(chain A and (resseq 3:31 or resseq 33:39 or resseq...A1 - 160
1111(chain A and (resseq 3:31 or resseq 33:39 or resseq...A1 - 160
1121(chain A and (resseq 3:31 or resseq 33:39 or resseq...A1 - 160
211(chain B and (resseq 3:31 or resseq 33:39 or resseq...B3 - 31
221(chain B and (resseq 3:31 or resseq 33:39 or resseq...B33 - 39
231(chain B and (resseq 3:31 or resseq 33:39 or resseq...B0
241(chain B and (resseq 3:31 or resseq 33:39 or resseq...B80 - 109
251(chain B and (resseq 3:31 or resseq 33:39 or resseq...B0
261(chain B and (resseq 3:31 or resseq 33:39 or resseq...B111 - 115
271(chain B and (resseq 3:31 or resseq 33:39 or resseq...B139
281(chain B and (resseq 3:31 or resseq 33:39 or resseq...B1 - 161
291(chain B and (resseq 3:31 or resseq 33:39 or resseq...B1 - 161
2101(chain B and (resseq 3:31 or resseq 33:39 or resseq...B1 - 161
2111(chain B and (resseq 3:31 or resseq 33:39 or resseq...B1 - 161
311(chain C and (resseq 3:31 or resseq 33:39 or resseq...C3 - 31
321(chain C and (resseq 3:31 or resseq 33:39 or resseq...C33 - 39
331(chain C and (resseq 3:31 or resseq 33:39 or resseq...C41 - 42
341(chain C and (resseq 3:31 or resseq 33:39 or resseq...C44 - 78
351(chain C and (resseq 3:31 or resseq 33:39 or resseq...C1 - 160
361(chain C and (resseq 3:31 or resseq 33:39 or resseq...C111 - 115
371(chain C and (resseq 3:31 or resseq 33:39 or resseq...C1 - 160
381(chain C and (resseq 3:31 or resseq 33:39 or resseq...C139
391(chain C and (resseq 3:31 or resseq 33:39 or resseq...C1 - 160
3101(chain C and (resseq 3:31 or resseq 33:39 or resseq...C1 - 160
3111(chain C and (resseq 3:31 or resseq 33:39 or resseq...C1 - 160
3121(chain C and (resseq 3:31 or resseq 33:39 or resseq...C1 - 160
411(chain D and (resseq 3:31 or resseq 33:39 or resseq...D3 - 31
421(chain D and (resseq 3:31 or resseq 33:39 or resseq...D33 - 39
431(chain D and (resseq 3:31 or resseq 33:39 or resseq...D41 - 42
441(chain D and (resseq 3:31 or resseq 33:39 or resseq...D44 - 78
451(chain D and (resseq 3:31 or resseq 33:39 or resseq...D1 - 160
461(chain D and (resseq 3:31 or resseq 33:39 or resseq...D111 - 115
471(chain D and (resseq 3:31 or resseq 33:39 or resseq...D1 - 160
481(chain D and (resseq 3:31 or resseq 33:39 or resseq...D139
491(chain D and (resseq 3:31 or resseq 33:39 or resseq...D1 - 160
4101(chain D and (resseq 3:31 or resseq 33:39 or resseq...D1 - 160
4111(chain D and (resseq 3:31 or resseq 33:39 or resseq...D1 - 160
4121(chain D and (resseq 3:31 or resseq 33:39 or resseq...D1 - 160
511(chain E and (resseq 3:31 or resseq 33:39 or resseq...E3 - 31
521(chain E and (resseq 3:31 or resseq 33:39 or resseq...E33 - 39
531(chain E and (resseq 3:31 or resseq 33:39 or resseq...E41 - 42
541(chain E and (resseq 3:31 or resseq 33:39 or resseq...E44 - 78
551(chain E and (resseq 3:31 or resseq 33:39 or resseq...E2 - 160
561(chain E and (resseq 3:31 or resseq 33:39 or resseq...E111 - 115
571(chain E and (resseq 3:31 or resseq 33:39 or resseq...E2 - 160
581(chain E and (resseq 3:31 or resseq 33:39 or resseq...E139
591(chain E and (resseq 3:31 or resseq 33:39 or resseq...E2 - 160
5101(chain E and (resseq 3:31 or resseq 33:39 or resseq...E2 - 160
5111(chain E and (resseq 3:31 or resseq 33:39 or resseq...E2 - 160
5121(chain E and (resseq 3:31 or resseq 33:39 or resseq...E2 - 160
611(chain F and (resseq 3:31 or resseq 33:39 or resseq...F3 - 31
621(chain F and (resseq 3:31 or resseq 33:39 or resseq...F33 - 39
631(chain F and (resseq 3:31 or resseq 33:39 or resseq...F0
641(chain F and (resseq 3:31 or resseq 33:39 or resseq...F80 - 109
651(chain F and (resseq 3:31 or resseq 33:39 or resseq...F0
661(chain F and (resseq 3:31 or resseq 33:39 or resseq...F111 - 115
671(chain F and (resseq 3:31 or resseq 33:39 or resseq...F139
681(chain F and (resseq 3:31 or resseq 33:39 or resseq...F2 - 161
691(chain F and (resseq 3:31 or resseq 33:39 or resseq...F2 - 161
6101(chain F and (resseq 3:31 or resseq 33:39 or resseq...F2 - 161
6111(chain F and (resseq 3:31 or resseq 33:39 or resseq...F2 - 161

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Components

#1: Protein
DotU family type IV/VI secretion system protein


Mass: 18782.424 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: EA685_02620, EA746_015130 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A429M4M7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 6000, 10 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.07255 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07255 Å / Relative weight: 1
Reflection twinOperator: l,k,-h-l / Fraction: 0.03
ReflectionResolution: 2.59→48.62 Å / Num. obs: 37828 / % possible obs: 95.8 % / Redundancy: 2.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.086 / Rrim(I) all: 0.153 / Net I/σ(I): 6.8 / Num. measured all: 109140 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.59-2.712.70.5271164543860.8460.3750.651.990.6
8.98-48.622.80.03825739090.9970.0260.04618.290.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.17data scaling
PHENIXv1.10refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.594→48.619 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.59
RfactorNum. reflection% reflection
Rfree0.2694 1988 5.26 %
Rwork0.2094 --
obs0.2125 37807 95.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.23 Å2 / Biso mean: 39.3929 Å2 / Biso min: 6.18 Å2
Refinement stepCycle: final / Resolution: 2.594→48.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7948 0 0 248 8196
Biso mean---27.53 -
Num. residues----960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018122
X-RAY DIFFRACTIONf_angle_d1.24810970
X-RAY DIFFRACTIONf_chiral_restr0.0681192
X-RAY DIFFRACTIONf_plane_restr0.011422
X-RAY DIFFRACTIONf_dihedral_angle_d16.5064838
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4234X-RAY DIFFRACTION14.118TORSIONAL
12B4234X-RAY DIFFRACTION14.118TORSIONAL
13C4234X-RAY DIFFRACTION14.118TORSIONAL
14D4234X-RAY DIFFRACTION14.118TORSIONAL
15E4234X-RAY DIFFRACTION14.118TORSIONAL
16F4234X-RAY DIFFRACTION14.118TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5979-2.6680.41641450.27972611275687
2.668-2.74620.4132960.27422818291494
2.7462-2.83460.34851370.26432832296994
2.8346-2.93550.32991630.24032758292192
2.9355-3.05250.33071260.24142825295193
3.0525-3.19080.33711190.22792770288993
3.1908-3.3580.26351500.20362785293592
3.358-3.5670.27181550.19452751290691
3.567-3.84010.2461810.18032696287790
3.8401-4.22230.20641430.17782727287090
4.2223-4.82360.2021330.1622761289491
4.8236-6.04110.2321710.20412736290790
6.0411-18.37620.3162920.21782804289691
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.78590.17540.40160.39831.01473.738-0.02460.1075-0.0479-0.02750.00180.06130.1159-0.04520.03350.2980.01020.00030.379-0.01290.128818.756-5.591117.5034
21.9457-0.2896-0.5460.69470.34660.93780.0451-0.1008-0.0643-0.07340.05380.01910.01540.0737-0.09420.2674-0.0143-0.0270.3820.00450.136-5.7735-5.938344.4413
31.86950.0308-1.0290.6497-0.39752.05020.1076-0.4211-0.10470.0847-0.0295-0.00880.0113-0.025-0.09070.2731-0.0679-0.04670.54190.01730.173320.9028-5.854158.6567
41.3881-0.1407-0.45120.885-0.16140.9430.06010.0428-0.0401-0.1448-0.03140.03750.0884-0.1248-0.00320.2944-0.0081-0.0490.32740.00420.11755.5112-5.755236.2885
51.261-0.16950.29320.3756-0.38863.1641-0.08420.2397-0.0191-0.0357-0.013-0.03040.0805-0.13230.09570.3563-0.0676-0.00510.51260.05360.154844.4559-5.50111.4825
62.477-0.45230.42180.79390.03961.74240.0738-0.0408-0.1559-0.105-0.00620.04430.07150.0098-0.07020.2920.0074-0.04580.40050.01580.131-7.698633.536217.3077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 160)A1 - 160
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 161)B1 - 161
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 160)C1 - 160
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 160)D1 - 160
5X-RAY DIFFRACTION5(chain 'E' and resid 2 through 160)E2 - 160
6X-RAY DIFFRACTION6(chain 'F' and resid 2 through 161)F2 - 161

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